Oh, wouldn't that just throw a wrench into all of this if he were alive? The four of them could start out all together and then Sammy would disappear and then they'd find out Jess is pregnant and John would be all, "get rid of it,"

And Jess would be NO FUCKING WAY.

So John makes Dean make a choice, go with him to find Sammy or stay with Jess and for the first time in his life Dean decides to go against his father's orders and stay with Jess. Because as far as he knows, his brother's dead, but his brother's baby is alive and he's going to do anything in his power to make sure it stays that way.